biohazard 1.0.4 → 1.1.0

raw patch · 8 files changed

+78/−40 lines, 8 filesdep ~exceptionsPVP ok

version bump matches the API change (PVP)

Dependency ranges changed: exceptions

API changes (from Hackage documentation)

Files

• CHANGELOG.md +27/−0
• biohazard.cabal +7/−6
• src/Bio/Bam/Reader.hs +6/−6
• src/Bio/Bam/Writer.hs +2/−3
• src/Bio/Iteratee.hs +3/−3
• src/Bio/Iteratee/Base.hs +4/−12
• src/Bio/Iteratee/IO.hs +9/−10
• src/Bio/Iteratee/Iteratee.hs +20/−0

@@ -0,0 +1,27 @@+# 1.1.0 (2018-10-12)++ * Work around changes in exceptions-0.10.0.  This version should+   compile cleanly and work with ghc-8.6.1.++# 1.0.4 (2018-09-02)++ * bugfix: memory leak in BGZF encoder++# 1.0.3 (2018-08-26)++ * bugfix: seeking had been broken for a while+ +# 1.0.2 (2018-07-08)++ * compatibility with ghc-8.4.1+ * bugfix: long headers were garbled when writing BAM files+ * more robust imports to avoid breakage when dependencies update+ +# 1.0.1 (2018-02-06)++ * Bugfix: merging of overlapping read pairs++# 1.0.0 (2018-01-28)++ * Removed dead code and failed experiments.  `biohazard` is now feature+   complete by decree.

@@ -1,5 +1,5 @@ Name:                biohazard-Version:             1.0.4+Version:             1.1.0 Synopsis:            bioinformatics support library Description:         This is a collection of modules I separated from                      various bioinformatics tools.@@ -8,6 +8,7 @@ Homepage:            https://bitbucket.org/ustenzel/biohazard License:             BSD3 License-File:        LICENSE+Extra-Source-Files:  CHANGELOG.md  Author:              Udo Stenzel Maintainer:          u.stenzel@web.de@@ -15,7 +16,7 @@  Cabal-version:       >= 1.10 Build-type:          Simple-Tested-with:         GHC == 7.8.4, GHC == 7.10.3, GHC == 8.0.2, GHC == 8.2.1, GHC == 8.4.1, GHC == 8.4.3+Tested-with:         GHC == 7.8.4, GHC == 7.10.3, GHC == 8.0.2, GHC == 8.2.1, GHC == 8.4.3, GHC == 8.6.1  source-repository head   type:     git@@ -57,14 +58,14 @@    Build-depends:       async                    >= 2.0 && < 2.3,                        attoparsec               >= 0.10 && < 0.14,-                       base                     >= 4.7 && < 4.12,+                       base                     >= 4.7 && < 4.13,                        base-prelude             == 1.2.0.*,                        bytestring               >= 0.10.2 && < 0.11,-                       containers               == 0.5.*,-                       exceptions               >= 0.6 && < 0.9,+                       containers               >= 0.5 && < 0.7,+                       exceptions               >= 0.6 && < 0.11,                        hashable                 >= 1.0 && < 1.3,                        primitive                >= 0.5 && < 0.7,-                       stm                      == 2.4.*,+                       stm                      >= 2.4 && < 2.6,                        text                     >= 1.0 && < 1.3,                        transformers             >= 0.4.1 && < 0.6,                        unix                     >= 2.5 && < 2.8,

@@ -78,7 +78,7 @@ decodeAnyBamOrSam :: MonadIO m => BamEnumeratee m a decodeAnyBamOrSam it = isBamOrSam >>= \k -> k it -decodeAnyBamOrSamFile :: (MonadIO m, MonadMask m)+decodeAnyBamOrSamFile :: MonadBracketIO m                       => FilePath -> (BamMeta -> Iteratee [BamRec] m a) -> m (Iteratee [BamRec] m a) decodeAnyBamOrSamFile fn k = enumFileRandom defaultBufSize fn (decodeAnyBamOrSam k) >>= run @@ -207,13 +207,13 @@ decodeAnyBam it = do mk <- isBam ; case mk of Just  k -> k it                                               Nothing -> fail "this isn't BAM." -decodeAnyBamFile :: (MonadIO m, MonadMask m) => FilePath -> (BamMeta -> Iteratee [BamRaw] m a) -> m (Iteratee [BamRaw] m a)+decodeAnyBamFile :: MonadBracketIO m => FilePath -> (BamMeta -> Iteratee [BamRaw] m a) -> m (Iteratee [BamRaw] m a) decodeAnyBamFile fn k = enumFileRandom defaultBufSize fn (decodeAnyBam k) >>= run -concatDefaultInputs :: (MonadIO m, MonadMask m) => Enumerator' BamMeta [BamRaw] m a+concatDefaultInputs :: MonadBracketIO m => Enumerator' BamMeta [BamRaw] m a concatDefaultInputs it0 = liftIO getArgs >>= \fs -> concatInputs fs it0 -concatInputs :: (MonadIO m, MonadMask m) => [FilePath] -> Enumerator' BamMeta [BamRaw] m a+concatInputs :: MonadBracketIO m => [FilePath] -> Enumerator' BamMeta [BamRaw] m a concatInputs [       ] = enumFd defaultBufSize stdInput . decodeAnyBam >=> run concatInputs (fp0:fps) = enum1 fp0 >=> go fps   where@@ -221,12 +221,12 @@     enum1 "-" = enumFd   defaultBufSize stdInput . decodeAnyBam >=> run     enum1  fp = enumFile defaultBufSize fp       . decodeAnyBam >=> run -mergeDefaultInputs :: (MonadIO m, MonadMask m)+mergeDefaultInputs :: MonadBracketIO m     => (BamMeta -> Enumeratee [BamRaw] [BamRaw] (Iteratee [BamRaw] m) a)     -> Enumerator' BamMeta [BamRaw] m a mergeDefaultInputs (?) it0 = liftIO getArgs >>= \fs -> mergeInputs (?) fs it0 -mergeInputs :: (MonadIO m, MonadMask m)+mergeInputs :: MonadBracketIO m     => (BamMeta -> Enumeratee [BamRaw] [BamRaw] (Iteratee [BamRaw] m) a)     -> [FilePath] -> Enumerator' BamMeta [BamRaw] m a mergeInputs  _  [        ] = \k -> enumFd defaultBufSize stdInput (decodeAnyBam k) >>= run

@@ -24,7 +24,6 @@ import Foreign.Marshal.Alloc        ( alloca ) import System.IO                    ( openBinaryFile, IOMode(..) ) -import qualified Control.Monad.Catch                as C import qualified Data.ByteString                    as B import qualified Data.ByteString.Char8              as S import qualified Data.Vector.Generic                as V@@ -119,8 +118,8 @@ -- | Writes BAM encoded stuff to a file. writeBamFile :: IsBamRec r => FilePath -> BamMeta -> Iteratee [r] IO () writeBamFile fp meta =-    C.bracket (liftIO $ openBinaryFile fp WriteMode)-              (liftIO . hClose)+    bracketIO (openBinaryFile fp WriteMode)+              (hClose)               (flip writeBamHandle meta)  -- | write BAM encoded stuff to stdout

@@ -121,13 +121,13 @@ type Enumerator' h eo m b = (h -> Iteratee eo m b) -> m (Iteratee eo m b) type Enumeratee' h ei eo m b = (h -> Iteratee eo m b) -> Iteratee ei m (Iteratee eo m b) -enumAuxFile :: (MonadIO m, MonadMask m) => FilePath -> Iteratee S.ByteString m a -> m a+enumAuxFile :: MonadBracketIO m => FilePath -> Iteratee S.ByteString m a -> m a enumAuxFile fp it = liftIO (findAuxFile fp) >>= \f -> enumFile defaultBufSize f it >>= run -enumDefaultInputs :: (MonadIO m, MonadMask m) => Enumerator S.ByteString m a+enumDefaultInputs :: MonadBracketIO m => Enumerator S.ByteString m a enumDefaultInputs it0 = liftIO getArgs >>= flip enumInputs it0 -enumInputs :: (MonadIO m, MonadMask m) => [FilePath] -> Enumerator S.ByteString m a+enumInputs :: MonadBracketIO m => [FilePath] -> Enumerator S.ByteString m a enumInputs [] = enumFd defaultBufSize stdInput enumInputs xs = go xs   where go ("-":fs) = enumFd defaultBufSize stdInput >=> go fs

@@ -169,24 +169,16 @@   instance NullPoint s => MonadTrans (Iteratee s) where-  lift m = Iteratee $ \onDone _ -> m >>= flip onDone (Chunk emptyP)+    lift m = Iteratee $ \onDone _ -> m >>= flip onDone (Chunk emptyP)  instance (MonadIO m, Nullable s, NullPoint s) => MonadIO (Iteratee s m) where-  liftIO = lift . liftIO+    liftIO = lift . liftIO -instance (MonadThrow m, Nullable s, NullPoint s) =>-  MonadThrow (Iteratee s m) where+instance (MonadThrow m, Nullable s, NullPoint s) => MonadThrow (Iteratee s m) where     throwM e    = lift $ CIO.throwM e -instance (MonadCatch m, Nullable s, NullPoint s) =>-  MonadCatch (Iteratee s m) where+instance (MonadCatch m, Nullable s, NullPoint s) => MonadCatch (Iteratee s m) where     m `catch` f = Iteratee $ \od oc -> runIter m od oc `CIO.catch` (\e -> runIter (f e) od oc)---- prior to exceptions-0.6, these were part of MonadCatch-instance (MonadMask m, Nullable s, NullPoint s) => MonadMask (Iteratee s m) where-    mask q      = Iteratee $ \od oc -> CIO.mask $ \u -> runIter (q $ ilift u) od oc-    uninterruptibleMask q = Iteratee $ \od oc -> CIO.uninterruptibleMask $ \u -> runIter (q $ ilift u) od oc-  -- |Send 'EOF' to the @Iteratee@ and disregard the unconsumed part of the -- stream.  If the iteratee is in an exception state, that exception is

@@ -15,10 +15,9 @@ where  import Bio.Iteratee.Iteratee-import Bio.Prelude hiding ( bracket, loop )-import Control.Monad.Catch ( MonadMask, bracket )-import Control.Monad.IO.Class ( MonadIO(..) )-import System.IO (SeekMode(..))+import Bio.Prelude       hiding ( bracket, loop )+import Control.Monad.IO.Class   ( MonadIO(..)   )+import System.IO                ( SeekMode(..)  )  import qualified Data.ByteString as B @@ -65,25 +64,25 @@   -enumFile' :: (MonadIO m, MonadMask m) =>+enumFile' :: MonadBracketIO m =>   (Int -> Fd -> Enumerator s m a)   -> Int -- ^Buffer size   -> FilePath   -> Enumerator s m a-enumFile' enumf bufsize filepath iter = bracket-  (liftIO $ openFd filepath ReadOnly Nothing defaultFileFlags)-  (liftIO . closeFd)+enumFile' enumf bufsize filepath iter = bracketIO+  (openFd filepath ReadOnly Nothing defaultFileFlags)+  (closeFd)   (flip (enumf bufsize) iter)  enumFile ::-  (MonadIO m, MonadMask m)+  MonadBracketIO m   => Int                 -- ^Buffer size   -> FilePath   -> Enumerator Bytes m a enumFile = enumFile' enumFd  enumFileRandom ::-  (MonadIO m, MonadMask m)+  MonadBracketIO m   => Int                 -- ^Buffer size   -> FilePath   -> Enumerator Bytes m a

@@ -18,6 +18,7 @@   ,mBind_   ,ioBind   ,ioBind_+  ,MonadBracketIO(..)   -- ** Chunkwise Iteratees   ,mapChunksM_   ,foldChunksM@@ -63,6 +64,7 @@  import Bio.Iteratee.Base import Bio.Prelude hiding (loop)+import Control.Monad.Catch as CIO import Control.Monad.IO.Class (MonadIO(..)) import Control.Monad.Trans.Class (MonadTrans(..)) @@ -285,6 +287,24 @@ infixl 1 `ioBind_` ioBind_ :: MonadIO m => IO a -> Iteratee s m b -> Iteratee s m b ioBind_ m b = Iteratee $ \onDone onCont -> liftIO m >> runIter b onDone onCont++-- | Runs an 'Iteratee' in between an 'IO' action to acquire a resource+-- and one to release it.  'Iteratee' can't be an instance of+-- 'CIO.MonadMask', so 'CIO.bracket' isn't defined for it.  However, if+-- we restrict the acquire/release actions to 'IO', which is the most+-- important use case anyway, we can directly implement this weaker+-- version.+class MonadIO m => MonadBracketIO m where+    bracketIO :: IO a -> (a -> IO b) -> (a -> m c) -> m c++instance MonadBracketIO IO where+    {-# INLINE bracketIO #-}+    bracketIO = CIO.bracket++instance (MonadBracketIO m, Nullable s) => MonadBracketIO (Iteratee s m) where+    {-# INLINE bracketIO #-}+    bracketIO acquire release use =+        Iteratee $ \od oc -> bracketIO acquire release (\h -> runIter (use h) od oc)  -- | Convert one stream into another with the supplied mapping function. -- This function operates on whole chunks at a time, contrasting to